How to get started with micromamba on HPC

This guide explains how to install micromamba, recreate a shared environment, and use it on a Slurm-based HPC cluster

1. Install Micromamba

Micromamba is a lightweight, standalone conda package manager—ideal for HPC systems.

Quick Install

# create a directory for micromamba
mkdir -p ~/micromamba # change this path as needed

# Download and install micromamba to ~/micromamba
curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj -C ~/micromamba

# Add installation to your shell config (~/.bashrc)
./micromamba/bin/micromamba shell init -s bash -r ~/micromamba  # this writes to your .bashrc file
# then restart your terminal!

Verify Installation

micromamba --version

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2. Install the Shared Environment

Once you have the environment.yml file from your collaborator:

# Create environment from the YAML file
micromamba create -f environment.yml

# Or specify a custom environment name
micromamba create -n my_env_name -f environment.yml

3. Verify the enviroment installation

Once the installation is complete, you can verify it by activating the environment and checking the installed packages:

micromamba activate my_env_name  # replace with your environment name

This will download and install all packages specified in the environment file.